Starting phenix.real_space_refine on Sun Jun 15 21:51:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ole_16956/06_2025/8ole_16956.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ole_16956/06_2025/8ole_16956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ole_16956/06_2025/8ole_16956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ole_16956/06_2025/8ole_16956.map" model { file = "/net/cci-nas-00/data/ceres_data/8ole_16956/06_2025/8ole_16956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ole_16956/06_2025/8ole_16956.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.067 sd= 0.425 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 11209 2.51 5 N 2976 2.21 5 O 3515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17757 Number of models: 1 Model: "" Number of chains: 3 Chain: "X" Number of atoms: 6107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6107 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 35, 'TRANS': 740} Chain: "Y" Number of atoms: 6107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6107 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 35, 'TRANS': 740} Chain: "Z" Number of atoms: 5543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5543 Classifications: {'peptide': 702} Link IDs: {'PTRANS': 25, 'TRANS': 676} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N GLY Y 156 " occ=0.65 ... (2 atoms not shown) pdb=" O GLY Y 156 " occ=0.65 residue: pdb=" N GLY Z 156 " occ=0.98 ... (2 atoms not shown) pdb=" O GLY Z 156 " occ=0.98 Time building chain proxies: 11.19, per 1000 atoms: 0.63 Number of scatterers: 17757 At special positions: 0 Unit cell: (115.24, 93.8, 210.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 3515 8.00 N 2976 7.00 C 11209 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.92 Conformation dependent library (CDL) restraints added in 3.2 seconds 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4280 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 32 sheets defined 28.7% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.46 Creating SS restraints... Processing helix chain 'X' and resid 1 through 12 Processing helix chain 'X' and resid 15 through 26 Processing helix chain 'X' and resid 193 through 197 removed outlier: 4.015A pdb=" N SER X 196 " --> pdb=" O ASN X 193 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL X 197 " --> pdb=" O TYR X 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 193 through 197' Processing helix chain 'X' and resid 212 through 222 removed outlier: 3.966A pdb=" N CYS X 216 " --> pdb=" O GLU X 212 " (cutoff:3.500A) Processing helix chain 'X' and resid 359 through 365 removed outlier: 4.128A pdb=" N ARG X 363 " --> pdb=" O SER X 359 " (cutoff:3.500A) Processing helix chain 'X' and resid 494 through 510 removed outlier: 3.997A pdb=" N GLU X 500 " --> pdb=" O ARG X 496 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU X 503 " --> pdb=" O GLY X 499 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU X 504 " --> pdb=" O GLU X 500 " (cutoff:3.500A) Processing helix chain 'X' and resid 515 through 520 removed outlier: 3.549A pdb=" N ASP X 519 " --> pdb=" O SER X 515 " (cutoff:3.500A) Processing helix chain 'X' and resid 526 through 531 Processing helix chain 'X' and resid 540 through 553 removed outlier: 3.792A pdb=" N LYS X 553 " --> pdb=" O MET X 549 " (cutoff:3.500A) Processing helix chain 'X' and resid 555 through 573 removed outlier: 3.560A pdb=" N ASN X 559 " --> pdb=" O SER X 555 " (cutoff:3.500A) Processing helix chain 'X' and resid 593 through 597 removed outlier: 3.666A pdb=" N GLN X 597 " --> pdb=" O VAL X 594 " (cutoff:3.500A) Processing helix chain 'X' and resid 606 through 626 removed outlier: 3.913A pdb=" N ARG X 618 " --> pdb=" O THR X 614 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU X 621 " --> pdb=" O ARG X 617 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA X 625 " --> pdb=" O LEU X 621 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR X 626 " --> pdb=" O LYS X 622 " (cutoff:3.500A) Processing helix chain 'X' and resid 632 through 647 removed outlier: 3.838A pdb=" N ILE X 636 " --> pdb=" O ASN X 632 " (cutoff:3.500A) Processing helix chain 'X' and resid 655 through 667 removed outlier: 3.867A pdb=" N GLU X 665 " --> pdb=" O THR X 661 " (cutoff:3.500A) Processing helix chain 'X' and resid 704 through 715 removed outlier: 4.129A pdb=" N ASP X 714 " --> pdb=" O ASP X 710 " (cutoff:3.500A) Processing helix chain 'X' and resid 723 through 731 Processing helix chain 'X' and resid 738 through 745 Processing helix chain 'X' and resid 748 through 759 removed outlier: 3.702A pdb=" N GLN X 758 " --> pdb=" O GLU X 754 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP X 759 " --> pdb=" O PHE X 755 " (cutoff:3.500A) Processing helix chain 'X' and resid 761 through 776 removed outlier: 4.521A pdb=" N ASN X 765 " --> pdb=" O PRO X 761 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU X 776 " --> pdb=" O MET X 772 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 12 removed outlier: 3.896A pdb=" N LEU Y 10 " --> pdb=" O TYR Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 29 Processing helix chain 'Y' and resid 120 through 124 Processing helix chain 'Y' and resid 182 through 184 No H-bonds generated for 'chain 'Y' and resid 182 through 184' Processing helix chain 'Y' and resid 209 through 211 No H-bonds generated for 'chain 'Y' and resid 209 through 211' Processing helix chain 'Y' and resid 212 through 222 Processing helix chain 'Y' and resid 497 through 510 Processing helix chain 'Y' and resid 514 through 522 Processing helix chain 'Y' and resid 539 through 553 removed outlier: 3.758A pdb=" N LYS Y 553 " --> pdb=" O MET Y 549 " (cutoff:3.500A) Processing helix chain 'Y' and resid 555 through 574 removed outlier: 3.744A pdb=" N SER Y 574 " --> pdb=" O ASP Y 570 " (cutoff:3.500A) Processing helix chain 'Y' and resid 589 through 594 Processing helix chain 'Y' and resid 607 through 619 Processing helix chain 'Y' and resid 620 through 625 Processing helix chain 'Y' and resid 632 through 647 removed outlier: 3.722A pdb=" N ILE Y 636 " --> pdb=" O ASN Y 632 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA Y 639 " --> pdb=" O ASP Y 635 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS Y 647 " --> pdb=" O THR Y 643 " (cutoff:3.500A) Processing helix chain 'Y' and resid 659 through 667 Processing helix chain 'Y' and resid 704 through 713 Processing helix chain 'Y' and resid 723 through 734 Processing helix chain 'Y' and resid 737 through 747 removed outlier: 3.568A pdb=" N ARG Y 746 " --> pdb=" O PHE Y 742 " (cutoff:3.500A) Processing helix chain 'Y' and resid 748 through 758 removed outlier: 4.263A pdb=" N LEU Y 752 " --> pdb=" O ASP Y 748 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLN Y 758 " --> pdb=" O GLU Y 754 " (cutoff:3.500A) Processing helix chain 'Y' and resid 762 through 774 removed outlier: 4.176A pdb=" N ARG Y 766 " --> pdb=" O ILE Y 762 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU Y 768 " --> pdb=" O ARG Y 764 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS Y 774 " --> pdb=" O LEU Y 770 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2 through 12 Processing helix chain 'Z' and resid 15 through 27 removed outlier: 3.872A pdb=" N GLN Z 23 " --> pdb=" O SER Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 193 through 197 removed outlier: 3.640A pdb=" N VAL Z 197 " --> pdb=" O TYR Z 194 " (cutoff:3.500A) Processing helix chain 'Z' and resid 212 through 221 Processing helix chain 'Z' and resid 359 through 364 removed outlier: 3.618A pdb=" N ARG Z 363 " --> pdb=" O SER Z 359 " (cutoff:3.500A) Processing helix chain 'Z' and resid 497 through 507 removed outlier: 3.967A pdb=" N GLU Z 503 " --> pdb=" O GLY Z 499 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU Z 504 " --> pdb=" O GLU Z 500 " (cutoff:3.500A) Processing helix chain 'Z' and resid 515 through 521 Processing helix chain 'Z' and resid 526 through 531 Processing helix chain 'Z' and resid 540 through 552 removed outlier: 3.519A pdb=" N MET Z 544 " --> pdb=" O ALA Z 540 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N MET Z 549 " --> pdb=" O ALA Z 545 " (cutoff:3.500A) Processing helix chain 'Z' and resid 557 through 572 Processing helix chain 'Z' and resid 589 through 594 removed outlier: 3.616A pdb=" N ASP Z 593 " --> pdb=" O SER Z 589 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL Z 594 " --> pdb=" O ALA Z 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 589 through 594' Processing helix chain 'Z' and resid 606 through 624 Processing helix chain 'Z' and resid 632 through 647 Processing helix chain 'Z' and resid 655 through 660 removed outlier: 3.636A pdb=" N ILE Z 659 " --> pdb=" O THR Z 655 " (cutoff:3.500A) Processing helix chain 'Z' and resid 660 through 665 Processing helix chain 'Z' and resid 704 through 714 Processing helix chain 'Z' and resid 723 through 733 Processing helix chain 'Z' and resid 737 through 746 Processing helix chain 'Z' and resid 748 through 760 removed outlier: 3.769A pdb=" N ASP Z 759 " --> pdb=" O PHE Z 755 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN Z 760 " --> pdb=" O ILE Z 756 " (cutoff:3.500A) Processing helix chain 'Z' and resid 761 through 773 Processing sheet with id=AA1, first strand: chain 'X' and resid 73 through 74 removed outlier: 4.211A pdb=" N ILE X 92 " --> pdb=" O THR X 105 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N THR X 105 " --> pdb=" O ILE X 92 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLU X 94 " --> pdb=" O LEU X 103 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU X 103 " --> pdb=" O GLU X 94 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N PHE X 140 " --> pdb=" O SER X 157 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER X 157 " --> pdb=" O PHE X 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 165 through 166 removed outlier: 3.515A pdb=" N TYR X 165 " --> pdb=" O LEU X 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 115 through 121 Processing sheet with id=AA4, first strand: chain 'X' and resid 175 through 180 Processing sheet with id=AA5, first strand: chain 'X' and resid 254 through 257 removed outlier: 6.955A pdb=" N GLU Y 264 " --> pdb=" O ILE X 256 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE Y 273 " --> pdb=" O ILE Y 464 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE Y 464 " --> pdb=" O ILE Y 273 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU Y 473 " --> pdb=" O VAL Y 368 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL Y 368 " --> pdb=" O LEU Y 473 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 270 through 274 Processing sheet with id=AA7, first strand: chain 'X' and resid 278 through 283 removed outlier: 3.735A pdb=" N ALA X 278 " --> pdb=" O LYS X 297 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER X 295 " --> pdb=" O THR X 280 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N TRP X 291 " --> pdb=" O SER X 340 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N PHE X 342 " --> pdb=" O TRP X 291 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N GLU X 293 " --> pdb=" O PHE X 342 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 300 through 307 removed outlier: 3.742A pdb=" N TYR X 303 " --> pdb=" O ALA X 314 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 354 through 357 current: chain 'X' and resid 402 through 415 removed outlier: 5.868A pdb=" N ARG X 427 " --> pdb=" O ALA X 407 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL X 409 " --> pdb=" O ARG X 425 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG X 425 " --> pdb=" O VAL X 409 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU X 411 " --> pdb=" O SER X 423 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER X 423 " --> pdb=" O LEU X 411 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR X 413 " --> pdb=" O LEU X 421 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU X 421 " --> pdb=" O THR X 413 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 420 through 432 current: chain 'Y' and resid 315 through 321 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 350 through 354 current: chain 'Y' and resid 419 through 423 Processing sheet with id=AA9, first strand: chain 'X' and resid 323 through 324 Processing sheet with id=AB1, first strand: chain 'X' and resid 384 through 386 Processing sheet with id=AB2, first strand: chain 'X' and resid 680 through 683 removed outlier: 3.773A pdb=" N ASN X 677 " --> pdb=" O ASP X 680 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Y' and resid 33 through 34 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 33 through 34 current: chain 'Z' and resid 290 through 297 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 290 through 297 current: chain 'Z' and resid 338 through 345 Processing sheet with id=AB4, first strand: chain 'Y' and resid 165 through 166 removed outlier: 3.529A pdb=" N TYR Y 165 " --> pdb=" O LEU Y 84 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Y' and resid 139 through 145 removed outlier: 3.728A pdb=" N LYS Y 139 " --> pdb=" O ILE Y 108 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE Y 108 " --> pdb=" O LYS Y 139 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR Y 105 " --> pdb=" O VAL Y 93 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N VAL Y 93 " --> pdb=" O THR Y 105 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU Y 107 " --> pdb=" O VAL Y 91 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL Y 91 " --> pdb=" O LEU Y 107 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Y' and resid 115 through 116 Processing sheet with id=AB7, first strand: chain 'Y' and resid 158 through 159 Processing sheet with id=AB8, first strand: chain 'Y' and resid 290 through 291 removed outlier: 3.713A pdb=" N PHE Y 328 " --> pdb=" O VAL Y 339 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Y' and resid 306 through 307 Processing sheet with id=AC1, first strand: chain 'Y' and resid 628 through 629 removed outlier: 3.850A pdb=" N GLU Y 629 " --> pdb=" O VAL Y 717 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER Y 719 " --> pdb=" O GLU Y 629 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Z' and resid 80 through 81 removed outlier: 3.896A pdb=" N ILE Z 208 " --> pdb=" O TRP Z 81 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Z' and resid 83 through 84 removed outlier: 6.368A pdb=" N ALA Z 166 " --> pdb=" O TYR Z 177 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR Z 177 " --> pdb=" O ALA Z 166 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N MET Z 168 " --> pdb=" O TYR Z 175 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR Z 175 " --> pdb=" O MET Z 168 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Z' and resid 93 through 96 Processing sheet with id=AC5, first strand: chain 'Z' and resid 102 through 108 removed outlier: 3.513A pdb=" N ALA Z 104 " --> pdb=" O VAL Z 143 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS Z 139 " --> pdb=" O ILE Z 108 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLY Z 156 " --> pdb=" O ASP Z 142 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL Z 144 " --> pdb=" O GLN Z 154 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLN Z 154 " --> pdb=" O VAL Z 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Z' and resid 112 through 116 removed outlier: 3.565A pdb=" N VAL Z 112 " --> pdb=" O ASN Z 132 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER Z 114 " --> pdb=" O VAL Z 130 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL Z 130 " --> pdb=" O SER Z 114 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Z' and resid 120 through 121 Processing sheet with id=AC8, first strand: chain 'Z' and resid 263 through 264 removed outlier: 3.540A pdb=" N LYS Z 263 " --> pdb=" O VAL Z 474 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL Z 474 " --> pdb=" O LYS Z 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'Z' and resid 267 through 268 Processing sheet with id=AD1, first strand: chain 'Z' and resid 273 through 275 Processing sheet with id=AD2, first strand: chain 'Z' and resid 302 through 307 Processing sheet with id=AD3, first strand: chain 'Z' and resid 319 through 321 removed outlier: 3.566A pdb=" N ASN Z 321 " --> pdb=" O TYR Z 350 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR Z 350 " --> pdb=" O ASN Z 321 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL Z 351 " --> pdb=" O PHE Z 428 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU Z 421 " --> pdb=" O THR Z 413 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR Z 413 " --> pdb=" O LEU Z 421 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N SER Z 423 " --> pdb=" O LEU Z 411 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU Z 411 " --> pdb=" O SER Z 423 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ARG Z 425 " --> pdb=" O VAL Z 409 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL Z 409 " --> pdb=" O ARG Z 425 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ARG Z 427 " --> pdb=" O ALA Z 407 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Z' and resid 381 through 382 Processing sheet with id=AD5, first strand: chain 'Z' and resid 690 through 692 removed outlier: 3.838A pdb=" N PHE Z 682 " --> pdb=" O VAL Z 675 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL Z 675 " --> pdb=" O PHE Z 682 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.61 Time building geometry restraints manager: 6.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3727 1.33 - 1.45: 4211 1.45 - 1.57: 10079 1.57 - 1.69: 0 1.69 - 1.81: 99 Bond restraints: 18116 Sorted by residual: bond pdb=" N GLU Y 434 " pdb=" CA GLU Y 434 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.04e-02 9.25e+03 1.16e+01 bond pdb=" N HIS Y 436 " pdb=" CA HIS Y 436 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.27e-02 6.20e+03 8.87e+00 bond pdb=" N THR X 181 " pdb=" CA THR X 181 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.41e-02 5.03e+03 6.71e+00 bond pdb=" N ARG Z 620 " pdb=" CA ARG Z 620 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.19e-02 7.06e+03 6.66e+00 bond pdb=" N TRP Z 102 " pdb=" CA TRP Z 102 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.22e-02 6.72e+03 6.55e+00 ... (remaining 18111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 24306 3.20 - 6.40: 283 6.40 - 9.60: 34 9.60 - 12.80: 1 12.80 - 16.00: 2 Bond angle restraints: 24626 Sorted by residual: angle pdb=" C THR Y 181 " pdb=" CA THR Y 181 " pdb=" CB THR Y 181 " ideal model delta sigma weight residual 110.17 126.17 -16.00 1.97e+00 2.58e-01 6.59e+01 angle pdb=" C THR X 181 " pdb=" CA THR X 181 " pdb=" CB THR X 181 " ideal model delta sigma weight residual 110.17 125.30 -15.13 1.97e+00 2.58e-01 5.90e+01 angle pdb=" C GLU Z 495 " pdb=" CA GLU Z 495 " pdb=" CB GLU Z 495 " ideal model delta sigma weight residual 115.79 108.69 7.10 1.19e+00 7.06e-01 3.56e+01 angle pdb=" C ARG Z 620 " pdb=" CA ARG Z 620 " pdb=" CB ARG Z 620 " ideal model delta sigma weight residual 110.88 103.40 7.48 1.57e+00 4.06e-01 2.27e+01 angle pdb=" C ASN X 229 " pdb=" N THR X 230 " pdb=" CA THR X 230 " ideal model delta sigma weight residual 122.08 129.02 -6.94 1.47e+00 4.63e-01 2.23e+01 ... (remaining 24621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 9885 17.95 - 35.91: 853 35.91 - 53.86: 139 53.86 - 71.81: 26 71.81 - 89.77: 10 Dihedral angle restraints: 10913 sinusoidal: 4291 harmonic: 6622 Sorted by residual: dihedral pdb=" C THR Y 181 " pdb=" N THR Y 181 " pdb=" CA THR Y 181 " pdb=" CB THR Y 181 " ideal model delta harmonic sigma weight residual -122.00 -148.18 26.18 0 2.50e+00 1.60e-01 1.10e+02 dihedral pdb=" C THR X 181 " pdb=" N THR X 181 " pdb=" CA THR X 181 " pdb=" CB THR X 181 " ideal model delta harmonic sigma weight residual -122.00 -141.11 19.11 0 2.50e+00 1.60e-01 5.84e+01 dihedral pdb=" N THR Y 181 " pdb=" C THR Y 181 " pdb=" CA THR Y 181 " pdb=" CB THR Y 181 " ideal model delta harmonic sigma weight residual 123.40 142.46 -19.06 0 2.50e+00 1.60e-01 5.82e+01 ... (remaining 10910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.185: 2806 0.185 - 0.371: 12 0.371 - 0.556: 0 0.556 - 0.741: 1 0.741 - 0.927: 1 Chirality restraints: 2820 Sorted by residual: chirality pdb=" CA THR Y 181 " pdb=" N THR Y 181 " pdb=" C THR Y 181 " pdb=" CB THR Y 181 " both_signs ideal model delta sigma weight residual False 2.53 1.60 0.93 2.00e-01 2.50e+01 2.15e+01 chirality pdb=" CA THR X 181 " pdb=" N THR X 181 " pdb=" C THR X 181 " pdb=" CB THR X 181 " both_signs ideal model delta sigma weight residual False 2.53 1.97 0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" CB ILE Z 686 " pdb=" CA ILE Z 686 " pdb=" CG1 ILE Z 686 " pdb=" CG2 ILE Z 686 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 2817 not shown) Planarity restraints: 3186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY X 67 " 0.049 5.00e-02 4.00e+02 7.51e-02 9.01e+00 pdb=" N PRO X 68 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO X 68 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO X 68 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP Y 100 " -0.014 2.00e-02 2.50e+03 2.96e-02 8.76e+00 pdb=" C ASP Y 100 " 0.051 2.00e-02 2.50e+03 pdb=" O ASP Y 100 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG Y 101 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU X 389 " -0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO X 390 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO X 390 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO X 390 " -0.038 5.00e-02 4.00e+02 ... (remaining 3183 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 42 2.22 - 2.89: 7676 2.89 - 3.56: 28014 3.56 - 4.23: 43419 4.23 - 4.90: 68983 Nonbonded interactions: 148134 Sorted by model distance: nonbonded pdb=" NH2 ARG Z 620 " pdb=" O ALA Z 684 " model vdw 1.554 3.120 nonbonded pdb=" O GLU Y 347 " pdb=" CZ ARG Y 429 " model vdw 1.931 3.270 nonbonded pdb=" OG SER Y 161 " pdb=" CG2 THR Y 181 " model vdw 2.023 3.460 nonbonded pdb=" OE1 GLU Y 347 " pdb=" NH2 ARG Y 429 " model vdw 2.028 3.120 nonbonded pdb=" CB ASN X 171 " pdb=" NH1 ARG X 210 " model vdw 2.066 3.520 ... (remaining 148129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'X' and (resid 1 through 29 or resid 73 through 221 or resid 253 through \ 776)) selection = (chain 'Y' and (resid 1 through 29 or resid 73 through 221 or resid 253 through \ 776)) selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 50.830 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.378 18117 Z= 0.357 Angle : 0.902 15.997 24626 Z= 0.507 Chirality : 0.057 0.927 2820 Planarity : 0.006 0.076 3186 Dihedral : 13.976 89.766 6633 Min Nonbonded Distance : 1.554 Molprobity Statistics. All-atom Clashscore : 30.06 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.61 % Favored : 87.08 % Rotamer: Outliers : 0.15 % Allowed : 0.50 % Favored : 99.35 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.16), residues: 2244 helix: -1.31 (0.20), residues: 566 sheet: -2.39 (0.21), residues: 527 loop : -3.37 (0.16), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP X 356 HIS 0.009 0.002 HIS Y 315 PHE 0.023 0.002 PHE X 505 TYR 0.042 0.002 TYR X 219 ARG 0.008 0.001 ARG X 429 Details of bonding type rmsd hydrogen bonds : bond 0.24680 ( 550) hydrogen bonds : angle 9.19458 ( 1524) covalent geometry : bond 0.00397 (18116) covalent geometry : angle 0.90202 (24626) Misc. bond : bond 0.37834 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 440 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 1 MET cc_start: 0.7339 (mmm) cc_final: 0.7093 (mmm) REVERT: X 10 LEU cc_start: 0.8545 (tt) cc_final: 0.8323 (tt) REVERT: X 18 LEU cc_start: 0.8166 (mt) cc_final: 0.7959 (mt) REVERT: X 40 PHE cc_start: 0.7288 (p90) cc_final: 0.6762 (p90) REVERT: X 100 ASP cc_start: 0.6010 (t0) cc_final: 0.5800 (t0) REVERT: X 219 TYR cc_start: 0.8100 (m-80) cc_final: 0.7567 (m-80) REVERT: X 222 ASN cc_start: 0.8331 (m-40) cc_final: 0.7958 (p0) REVERT: X 242 ASP cc_start: 0.8032 (t0) cc_final: 0.7758 (t0) REVERT: X 265 MET cc_start: 0.3859 (mpp) cc_final: 0.3402 (mpp) REVERT: X 291 TRP cc_start: 0.7283 (m-10) cc_final: 0.6825 (m-10) REVERT: X 296 PHE cc_start: 0.7621 (m-10) cc_final: 0.7362 (m-10) REVERT: X 317 THR cc_start: 0.6420 (m) cc_final: 0.6205 (m) REVERT: X 333 LEU cc_start: 0.8836 (tt) cc_final: 0.8523 (mt) REVERT: X 347 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8009 (mm-30) REVERT: X 410 THR cc_start: 0.8058 (m) cc_final: 0.7362 (p) REVERT: X 447 LEU cc_start: 0.8069 (tp) cc_final: 0.7826 (tt) REVERT: X 494 LEU cc_start: 0.9137 (tp) cc_final: 0.8668 (tp) REVERT: X 527 MET cc_start: 0.6973 (mtm) cc_final: 0.6484 (mtm) REVERT: X 530 MET cc_start: 0.7645 (ptt) cc_final: 0.7250 (ptt) REVERT: X 531 PHE cc_start: 0.8250 (m-80) cc_final: 0.7769 (m-80) REVERT: X 544 MET cc_start: 0.7588 (mmp) cc_final: 0.7361 (mmp) REVERT: X 552 PHE cc_start: 0.8230 (t80) cc_final: 0.7508 (t80) REVERT: X 615 ILE cc_start: 0.8266 (pt) cc_final: 0.7946 (mt) REVERT: X 667 PHE cc_start: 0.7364 (m-10) cc_final: 0.6384 (m-10) REVERT: X 727 LEU cc_start: 0.8577 (mp) cc_final: 0.8366 (mt) REVERT: X 755 PHE cc_start: 0.7833 (m-80) cc_final: 0.7185 (m-10) REVERT: X 772 MET cc_start: 0.8498 (mtm) cc_final: 0.7799 (mtm) REVERT: X 773 GLN cc_start: 0.8853 (pt0) cc_final: 0.8625 (pt0) REVERT: X 774 CYS cc_start: 0.5812 (p) cc_final: 0.5592 (p) REVERT: Y 5 ILE cc_start: 0.8433 (mt) cc_final: 0.7956 (mt) REVERT: Y 75 ASN cc_start: 0.8126 (p0) cc_final: 0.7804 (p0) REVERT: Y 94 GLU cc_start: 0.7743 (tt0) cc_final: 0.7083 (tm-30) REVERT: Y 116 ASN cc_start: 0.7853 (m-40) cc_final: 0.7265 (t0) REVERT: Y 128 LEU cc_start: 0.7082 (tt) cc_final: 0.6537 (pp) REVERT: Y 142 ASP cc_start: 0.7332 (t0) cc_final: 0.6876 (t0) REVERT: Y 170 HIS cc_start: 0.7993 (t70) cc_final: 0.7605 (t70) REVERT: Y 297 LYS cc_start: 0.8350 (mmpt) cc_final: 0.8112 (mmtm) REVERT: Y 350 TYR cc_start: 0.7503 (m-10) cc_final: 0.6476 (m-10) REVERT: Y 371 LEU cc_start: 0.8169 (pt) cc_final: 0.7945 (pt) REVERT: Y 414 GLN cc_start: 0.6920 (mp10) cc_final: 0.6035 (mp10) REVERT: Y 422 ASN cc_start: 0.7937 (t0) cc_final: 0.7368 (t0) REVERT: Y 444 LEU cc_start: 0.8513 (tp) cc_final: 0.7891 (pp) REVERT: Y 530 MET cc_start: 0.7663 (tpt) cc_final: 0.6931 (tpt) REVERT: Y 591 TRP cc_start: 0.8047 (m-90) cc_final: 0.7306 (m-90) REVERT: Y 617 ARG cc_start: 0.8697 (tpm170) cc_final: 0.8356 (tpm170) REVERT: Y 673 TYR cc_start: 0.6535 (m-80) cc_final: 0.6312 (m-80) REVERT: Y 694 LYS cc_start: 0.7623 (mmmt) cc_final: 0.7146 (mmmt) REVERT: Y 762 ILE cc_start: 0.8166 (pt) cc_final: 0.7738 (pt) REVERT: Z 1 MET cc_start: 0.7864 (tmm) cc_final: 0.7558 (tmm) REVERT: Z 9 LEU cc_start: 0.8371 (tp) cc_final: 0.8035 (mt) REVERT: Z 11 THR cc_start: 0.8201 (m) cc_final: 0.7079 (m) REVERT: Z 14 TYR cc_start: 0.7601 (p90) cc_final: 0.6820 (p90) REVERT: Z 94 GLU cc_start: 0.7926 (mp0) cc_final: 0.7586 (mp0) REVERT: Z 199 MET cc_start: 0.8632 (mmp) cc_final: 0.8238 (mmp) REVERT: Z 215 LYS cc_start: 0.7870 (mppt) cc_final: 0.7070 (mmtt) REVERT: Z 219 TYR cc_start: 0.7288 (m-10) cc_final: 0.6951 (m-80) REVERT: Z 267 TYR cc_start: 0.7359 (m-80) cc_final: 0.6928 (m-80) REVERT: Z 464 ILE cc_start: 0.9080 (mp) cc_final: 0.8123 (mp) REVERT: Z 500 GLU cc_start: 0.8565 (pp20) cc_final: 0.8250 (pp20) REVERT: Z 527 MET cc_start: 0.7921 (ptm) cc_final: 0.7604 (ppp) REVERT: Z 530 MET cc_start: 0.9054 (tpt) cc_final: 0.8711 (tpp) REVERT: Z 549 MET cc_start: 0.7869 (ppp) cc_final: 0.7591 (ppp) REVERT: Z 617 ARG cc_start: 0.8118 (ptm160) cc_final: 0.7895 (ptm160) REVERT: Z 623 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8219 (tp30) REVERT: Z 721 ILE cc_start: 0.7916 (mp) cc_final: 0.7304 (mp) outliers start: 3 outliers final: 0 residues processed: 443 average time/residue: 0.4537 time to fit residues: 290.8709 Evaluate side-chains 380 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 379 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 175 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 130 optimal weight: 0.0970 chunk 203 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 180 GLN X 183 ASN ** X 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 302 GLN Y 97 ASN ** Y 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 457 ASN Z 8 GLN ** Z 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 769 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.145683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.113397 restraints weight = 51680.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.118129 restraints weight = 36741.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.121901 restraints weight = 27827.832| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 18117 Z= 0.185 Angle : 0.792 9.810 24626 Z= 0.415 Chirality : 0.050 0.191 2820 Planarity : 0.006 0.071 3186 Dihedral : 6.627 24.972 2447 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 23.62 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.61 % Favored : 87.12 % Rotamer: Outliers : 0.10 % Allowed : 6.38 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.16), residues: 2244 helix: -1.12 (0.20), residues: 572 sheet: -2.50 (0.21), residues: 503 loop : -3.29 (0.16), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP Y 262 HIS 0.010 0.002 HIS Y 170 PHE 0.031 0.002 PHE Y 505 TYR 0.029 0.002 TYR X 219 ARG 0.005 0.001 ARG Z 274 Details of bonding type rmsd hydrogen bonds : bond 0.05321 ( 550) hydrogen bonds : angle 7.19051 ( 1524) covalent geometry : bond 0.00400 (18116) covalent geometry : angle 0.79235 (24626) Misc. bond : bond 0.00303 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 426 time to evaluate : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 18 LEU cc_start: 0.8366 (mt) cc_final: 0.8149 (mt) REVERT: X 24 GLU cc_start: 0.8757 (pt0) cc_final: 0.8556 (pt0) REVERT: X 40 PHE cc_start: 0.7934 (p90) cc_final: 0.7416 (p90) REVERT: X 70 GLN cc_start: 0.7757 (mp10) cc_final: 0.7283 (mp10) REVERT: X 75 ASN cc_start: 0.8596 (p0) cc_final: 0.8099 (p0) REVERT: X 100 ASP cc_start: 0.6593 (t0) cc_final: 0.6211 (t0) REVERT: X 194 TYR cc_start: 0.7423 (m-10) cc_final: 0.7175 (m-10) REVERT: X 219 TYR cc_start: 0.8639 (m-80) cc_final: 0.8325 (m-80) REVERT: X 222 ASN cc_start: 0.8986 (m-40) cc_final: 0.8480 (p0) REVERT: X 251 ASN cc_start: 0.7975 (m110) cc_final: 0.7628 (m110) REVERT: X 265 MET cc_start: 0.4994 (mpp) cc_final: 0.4490 (mpp) REVERT: X 356 TRP cc_start: 0.6794 (m100) cc_final: 0.6241 (m100) REVERT: X 375 LEU cc_start: 0.8300 (mm) cc_final: 0.7980 (mm) REVERT: X 385 TYR cc_start: 0.8284 (t80) cc_final: 0.8029 (t80) REVERT: X 394 TRP cc_start: 0.8218 (m-10) cc_final: 0.7949 (m-10) REVERT: X 477 ASN cc_start: 0.8770 (p0) cc_final: 0.8468 (p0) REVERT: X 527 MET cc_start: 0.8397 (mtm) cc_final: 0.7430 (mtm) REVERT: X 549 MET cc_start: 0.9290 (mpp) cc_final: 0.9012 (mmm) REVERT: X 552 PHE cc_start: 0.9034 (t80) cc_final: 0.7924 (t80) REVERT: X 620 ARG cc_start: 0.9165 (ptm-80) cc_final: 0.8904 (ptm-80) REVERT: X 623 GLU cc_start: 0.8466 (mp0) cc_final: 0.7936 (mm-30) REVERT: X 666 LYS cc_start: 0.8584 (ptmm) cc_final: 0.8160 (tptp) REVERT: X 673 TYR cc_start: 0.8299 (m-80) cc_final: 0.7943 (m-80) REVERT: X 718 ILE cc_start: 0.7945 (mp) cc_final: 0.7704 (tt) REVERT: X 727 LEU cc_start: 0.8885 (mp) cc_final: 0.8652 (mt) REVERT: X 748 ASP cc_start: 0.8986 (t0) cc_final: 0.8661 (t0) REVERT: X 755 PHE cc_start: 0.8509 (m-80) cc_final: 0.7862 (m-10) REVERT: X 772 MET cc_start: 0.8767 (mtm) cc_final: 0.8307 (mtm) REVERT: X 773 GLN cc_start: 0.9095 (pt0) cc_final: 0.8871 (pt0) REVERT: Y 69 TYR cc_start: 0.8095 (m-80) cc_final: 0.7707 (m-80) REVERT: Y 75 ASN cc_start: 0.8798 (p0) cc_final: 0.8519 (p0) REVERT: Y 94 GLU cc_start: 0.8237 (tt0) cc_final: 0.7032 (tm-30) REVERT: Y 102 TRP cc_start: 0.7629 (m-90) cc_final: 0.7060 (m-90) REVERT: Y 116 ASN cc_start: 0.8203 (m-40) cc_final: 0.7767 (t0) REVERT: Y 128 LEU cc_start: 0.8050 (tt) cc_final: 0.7319 (pp) REVERT: Y 142 ASP cc_start: 0.7635 (t0) cc_final: 0.6960 (t0) REVERT: Y 155 TYR cc_start: 0.7965 (m-10) cc_final: 0.7741 (m-10) REVERT: Y 170 HIS cc_start: 0.8538 (t70) cc_final: 0.7906 (t70) REVERT: Y 204 ASP cc_start: 0.8547 (m-30) cc_final: 0.8329 (m-30) REVERT: Y 265 MET cc_start: 0.8066 (mmp) cc_final: 0.7302 (tpt) REVERT: Y 267 TYR cc_start: 0.7198 (m-10) cc_final: 0.6653 (m-10) REVERT: Y 277 PHE cc_start: 0.7594 (t80) cc_final: 0.7048 (t80) REVERT: Y 297 LYS cc_start: 0.8451 (mmpt) cc_final: 0.8004 (mmtm) REVERT: Y 356 TRP cc_start: 0.6854 (m-10) cc_final: 0.6244 (m-90) REVERT: Y 405 HIS cc_start: 0.8338 (p90) cc_final: 0.8073 (p90) REVERT: Y 422 ASN cc_start: 0.8589 (t0) cc_final: 0.8302 (t0) REVERT: Y 444 LEU cc_start: 0.9054 (tp) cc_final: 0.8514 (pp) REVERT: Y 462 TYR cc_start: 0.6491 (m-80) cc_final: 0.4803 (m-80) REVERT: Y 512 ILE cc_start: 0.8716 (pt) cc_final: 0.8479 (pt) REVERT: Y 530 MET cc_start: 0.8246 (tpt) cc_final: 0.7437 (tpt) REVERT: Y 591 TRP cc_start: 0.8442 (m-90) cc_final: 0.7593 (m-90) REVERT: Y 611 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8420 (pm20) REVERT: Y 617 ARG cc_start: 0.8721 (tpm170) cc_final: 0.8485 (tpm170) REVERT: Y 762 ILE cc_start: 0.8476 (pt) cc_final: 0.8045 (pt) REVERT: Z 14 TYR cc_start: 0.8152 (p90) cc_final: 0.7400 (p90) REVERT: Z 189 TYR cc_start: 0.9433 (m-10) cc_final: 0.9188 (m-10) REVERT: Z 199 MET cc_start: 0.8725 (mmp) cc_final: 0.7967 (tmm) REVERT: Z 215 LYS cc_start: 0.7443 (mppt) cc_final: 0.6879 (mmtt) REVERT: Z 219 TYR cc_start: 0.7635 (m-10) cc_final: 0.7155 (m-80) REVERT: Z 267 TYR cc_start: 0.8083 (m-80) cc_final: 0.7257 (m-80) REVERT: Z 276 LYS cc_start: 0.7536 (tptt) cc_final: 0.7098 (tttt) REVERT: Z 301 TYR cc_start: 0.7839 (m-10) cc_final: 0.7308 (m-10) REVERT: Z 342 PHE cc_start: 0.6634 (t80) cc_final: 0.6381 (t80) REVERT: Z 464 ILE cc_start: 0.9247 (mp) cc_final: 0.8739 (mp) REVERT: Z 500 GLU cc_start: 0.8671 (pp20) cc_final: 0.8365 (pp20) REVERT: Z 527 MET cc_start: 0.8430 (ptm) cc_final: 0.7910 (pmm) REVERT: Z 530 MET cc_start: 0.8965 (tpt) cc_final: 0.8669 (tpp) REVERT: Z 549 MET cc_start: 0.8296 (ppp) cc_final: 0.7868 (ppp) REVERT: Z 550 LYS cc_start: 0.8337 (mmpt) cc_final: 0.7677 (mttm) REVERT: Z 617 ARG cc_start: 0.8086 (ptm160) cc_final: 0.7786 (ptm160) REVERT: Z 623 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8364 (mm-30) REVERT: Z 624 MET cc_start: 0.7829 (ptp) cc_final: 0.7369 (ptp) REVERT: Z 673 TYR cc_start: 0.7943 (m-10) cc_final: 0.7406 (m-10) REVERT: Z 721 ILE cc_start: 0.7822 (mp) cc_final: 0.7163 (mp) outliers start: 2 outliers final: 0 residues processed: 428 average time/residue: 0.3610 time to fit residues: 222.1218 Evaluate side-chains 374 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 373 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.6668 > 50: distance: 61 - 65: 27.578 distance: 65 - 66: 20.720 distance: 66 - 67: 26.426 distance: 66 - 69: 17.244 distance: 67 - 68: 14.631 distance: 67 - 73: 15.388 distance: 69 - 70: 12.369 distance: 70 - 71: 18.736 distance: 70 - 72: 25.736 distance: 73 - 74: 36.656 distance: 73 - 200: 29.645 distance: 74 - 75: 14.854 distance: 74 - 77: 17.696 distance: 75 - 76: 12.161 distance: 75 - 83: 37.277 distance: 76 - 197: 23.214 distance: 77 - 78: 12.819 distance: 78 - 79: 11.400 distance: 78 - 80: 9.202 distance: 79 - 81: 6.174 distance: 80 - 82: 13.080 distance: 83 - 84: 11.094 distance: 84 - 85: 4.884 distance: 84 - 87: 46.759 distance: 85 - 86: 22.236 distance: 85 - 89: 21.729 distance: 87 - 88: 27.406 distance: 89 - 90: 29.888 distance: 89 - 178: 29.922 distance: 90 - 91: 45.004 distance: 90 - 93: 29.944 distance: 91 - 92: 39.344 distance: 91 - 94: 55.943 distance: 94 - 95: 40.794 distance: 95 - 96: 37.618 distance: 96 - 97: 27.390 distance: 96 - 98: 19.156 distance: 98 - 99: 10.383 distance: 99 - 100: 7.209 distance: 99 - 102: 18.148 distance: 100 - 101: 21.914 distance: 100 - 105: 11.254 distance: 102 - 103: 30.227 distance: 102 - 104: 29.611 distance: 105 - 106: 8.651 distance: 106 - 107: 15.438 distance: 106 - 109: 27.054 distance: 107 - 108: 28.773 distance: 107 - 112: 16.717 distance: 109 - 110: 15.387 distance: 109 - 111: 21.989 distance: 112 - 113: 8.565 distance: 113 - 114: 24.632 distance: 113 - 116: 29.442 distance: 114 - 115: 8.941 distance: 114 - 120: 23.364 distance: 116 - 117: 15.499 distance: 117 - 118: 7.481 distance: 117 - 119: 10.456 distance: 120 - 121: 20.500 distance: 121 - 122: 29.050 distance: 121 - 124: 29.713 distance: 122 - 123: 19.918 distance: 122 - 126: 19.338 distance: 124 - 125: 27.721 distance: 126 - 127: 21.697 distance: 127 - 128: 15.126 distance: 127 - 130: 13.309 distance: 128 - 129: 15.620 distance: 128 - 133: 14.327 distance: 130 - 131: 55.092